Started on 2025-01-15 17:26:49

Explanation of all the statistics given by ipdSummary:

motifs.gff score - Phred-transformed pvalue that a kinetic deviation exists at this position IPDratio - interpulse duration ratio: capped mean of normalized IPDs observed at this position/ normalized mean IPD predicted by the synthetic control model for this sequence context, > 1 - the sequencing polymerase slowed down, < 1 the sequencing polymerase sped up context - 20bp before and 20bp after the modified base identificationQv - the phred-transformed probability of an incorrect identification. Low indicates higher probability of an error. coverage - count of valid IPDs at this position

basemods.csv tpl - 1-based template position tMean - capped mean of normalized IPDs observed at this position modelPrediction - normalized mean IPD predicted by the synthetic control model for this sequence context

For whole genome amplification, the statistical test used is a case-control, two-sample t-test.

https://github.com/PacificBiosciences/kineticsTools/blob/master/doc/manual.rst

QC

Plotting IPDratio by score

Plotting IPDratio by coverage

Plotting IPDratio by score categories

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

## `summarise()` has grouped output by 'scoreCats'. You can override using the
## `.groups` argument.

Analysis

Number of 6mA and 4mC methylation sites per sample

## `summarise()` has grouped output by 'Name', 'condition', 'feature'. You can
## override using the `.groups` argument.
## `summarise()` has grouped output by 'Name', 'condition', 'feature'. You can
## override using the `.groups` argument.

Number of genes with 6mA or 4mC modifications

## `summarise()` has grouped output by 'Name', 'condition'. You can override using
## the `.groups` argument.

Sharing of 6mA or 4mC modified sites